Bitbow: a digital format of Brainbow enables highly efficient neuronal lineage tracing and morphology reconstruction in single brains

2020 ◽  
Author(s):  
Ye Li ◽  
Logan A Walker ◽  
Yimeng Zhao ◽  
Erica M Edwards ◽  
Nigel S Michki ◽  
...  
Keyword(s):  
Lineage Tracing ◽  
Neuronal Morphology ◽  
Statistical Tools ◽  
Color Palette ◽  
Sparse Labeling ◽  
Digital Format ◽  
Neuronal Lineage ◽  
Spectrally Resolved ◽  
Network Patterns ◽  
Axonal Arbors

AbstractIdentifying the cellular origins and mapping the dendritic and axonal arbors of neurons have been century old quests to understand the heterogeneity among these brain cells. Classical chemical and genetic methods take advantage of light microscopy and sparse labeling to unambiguously, albeit inefficiently, trace a few neuronal lineages or reconstruct their morphologies in each sampled brain. To improve the analysis throughput, we designed Bitbow, a digital format of Brainbow which exponentially expands the color palette to provide tens of thousands of spectrally resolved unique labels. We generated transgenic Bitbow Drosophila lines, established statistical tools, and streamlined sample preparation, image processing and data analysis pipelines to allow conveniently mapping neural lineages, studying neuronal morphology and revealing neural network patterns with an unprecedented speed, scale and resolution.

scholarly journals New Mouse Lines for the Analysis of Neuronal Morphology Using CreER(T)/loxP-Directed Sparse Labeling

PLoS ONE ◽  
2009 ◽  
Vol 4 (11) ◽  
pp. e7859 ◽  
Author(s):  
Tudor C. Badea ◽  
Zhong L. Hua ◽  
Philip M. Smallwood ◽  
John Williams ◽  
Thomas Rotolo ◽  
...  
Keyword(s):  
Neuronal Morphology ◽  
Sparse Labeling ◽  
Mouse Lines

scholarly journals Tumor cells generate astrocyte-like cells that contribute to SHH-driven medulloblastoma relapse

2021 ◽  
Vol 218 (9) ◽  
Author(s):  
Duancheng Guo ◽  
Yuan Wang ◽  
Yan Cheng ◽  
Shengyou Liao ◽  
Jian Hu ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Bone Morphogenetic Proteins ◽  
Critical Role ◽  
Pediatric Brain Tumor ◽  
Lineage Tracing ◽  
Bmp Signaling ◽  
Cell Transdifferentiation ◽  
Neuronal Lineage ◽  
Pediatric Brain ◽  
The Brain

Astrocytes, a major glial cell type in the brain, play a critical role in supporting the progression of medulloblastoma (MB), the most common malignant pediatric brain tumor. Through lineage tracing analyses and single-cell RNA sequencing, we demonstrate that astrocytes are predominantly derived from the transdifferentiation of tumor cells in relapsed MB (but not in primary MB), although MB cells are generally believed to be neuronal-lineage committed. Such transdifferentiation of MB cells relies on Sox9, a transcription factor critical for gliogenesis. Our studies further reveal that bone morphogenetic proteins (BMPs) stimulate the transdifferentiation of MB cells by inducing the phosphorylation of Sox9. Pharmacological inhibition of BMP signaling represses MB cell transdifferentiation into astrocytes and suppresses tumor relapse. Our studies establish the distinct cellular sources of astrocytes in primary and relapsed MB and provide an avenue to prevent and treat MB relapse by targeting tumor cell transdifferentiation.

scholarly journals Neuronal morphology and projection analysis by multispectral tracing in densely labeled mouse brain

2017 ◽  
Author(s):  
Douglas H. Roossien ◽  
John M. Webb ◽  
Benjamin V. Sadis ◽  
Yan Yan ◽  
Lia Y. Min ◽  
...  
Keyword(s):  
Light Microscopy ◽  
Long Range ◽  
Mouse Brain ◽  
Cell Morphology ◽  
Brain Function ◽  
Neuronal Morphology ◽  
Neuronal Populations ◽  
Sparse Labeling ◽  
Projection Analysis ◽  
Imagej Plugin

AbstractAccurate and complete neuronal wiring diagrams are necessary for understanding brain function at many scales from long-range interregional projections to microcircuits. Traditionally, light microscopy-based anatomical reconstructions use monochromatic labeling and therefore necessitate sparse labeling to eliminate tracing ambiguity between intermingled neurons. Consequently, our knowledge of neuronal morphology has largely been based on averaged estimations across many samples. Recently developed second-generation Brainbow tools promise to circumvent this limitation by revealing fine anatomical details of many unambiguously identifiable neurons in densely labeled samples. Yet, a means to quantify and analyze the information is currently lacking. Therefore, we developed nTracer, an ImageJ plugin capable of rapidly and accurately reconstructing whole-cell morphology of large neuronal populations in densely labeled brains.

scholarly journals Dense reconstruction of elongated cell lineages: overcoming suboptimum lineage encoding and sparse cell sampling

2020 ◽  
Author(s):  
Ken Sugino ◽  
Rosa L. Miyares ◽  
Isabel Espinosa-Medina ◽  
Hui-Min Chen ◽  
Christopher J Potter ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Lineage Tracing ◽  
Simple Method ◽  
Cell Lineages ◽  
Stem Cell Divisions ◽  
Neuronal Lineage ◽  
Dense Reconstruction ◽  
Parameter Ranges ◽  
Neuronal Diversification

AbstractAcquiring both lineage and cell-type information during brain development could elucidate transcriptional programs underling neuronal diversification. This is now feasible with single-cell RNA-seq combined with CRISPR-based lineage tracing, which generates genetic barcodes with cumulative CRISPR edits. This technique has not yet been optimized to deliver high-resolution lineage reconstruction of protracted lineages. Drosophila neuronal lineages are an ideal model to consider, as multiple lineages have been morphologically mapped at single-cell resolution. Here we find the parameter ranges required to encode a representative neuronal lineage emanating from 100 stem cell divisions. We derive the optimum editing rate to be inversely proportional to lineage depth, enabling encoding to persist across lineage progression. Further, we experimentally determine the editing rates of a Cas9-deaminase in cycling neural stem cells, finding near ideal rates to map elongated Drosophila neuronal lineages. Moreover, we propose and evaluate strategies to separate recurring cell-types for lineage reconstruction. Finally, we present a simple method to combine multiple experiments, which permits dense reconstruction of protracted cell lineages despite suboptimum lineage encoding and sparse cell sampling.

scholarly journals Genetically-Directed, Cell Type-Specific Sparse Labeling for the Analysis of Neuronal Morphology

PLoS ONE ◽  
2008 ◽  
Vol 3 (12) ◽  
pp. e4099 ◽  
Author(s):  
Thomas Rotolo ◽  
Philip M. Smallwood ◽  
John Williams ◽  
Jeremy Nathans
Keyword(s):  
Neuronal Morphology ◽  
Cell Type ◽  
Sparse Labeling ◽  
Cell Type Specific

Fluorescent proteins for in vivo imaging, where's the biliverdin?

2020 ◽  
Vol 48 (6) ◽  
pp. 2657-2667
Author(s):  
Felipe Montecinos-Franjola ◽  
John Y. Lin ◽  
Erik A. Rodriguez
Keyword(s):  
Hydrogen Peroxide ◽  
In Vivo Imaging ◽  
Near Infrared ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Fluorescent Imaging ◽  
Infrared Light ◽  
Red Fluorescent Protein ◽  
Color Palette

Noninvasive fluorescent imaging requires far-red and near-infrared fluorescent proteins for deeper imaging. Near-infrared light penetrates biological tissue with blood vessels due to low absorbance, scattering, and reflection of light and has a greater signal-to-noise due to less autofluorescence. Far-red and near-infrared fluorescent proteins absorb light >600 nm to expand the color palette for imaging multiple biosensors and noninvasive in vivo imaging. The ideal fluorescent proteins are bright, photobleach minimally, express well in the desired cells, do not oligomerize, and generate or incorporate exogenous fluorophores efficiently. Coral-derived red fluorescent proteins require oxygen for fluorophore formation and release two hydrogen peroxide molecules. New fluorescent proteins based on phytochrome and phycobiliproteins use biliverdin IXα as fluorophores, do not require oxygen for maturation to image anaerobic organisms and tumor core, and do not generate hydrogen peroxide. The small Ultra-Red Fluorescent Protein (smURFP) was evolved from a cyanobacterial phycobiliprotein to covalently attach biliverdin as an exogenous fluorophore. The small Ultra-Red Fluorescent Protein is biophysically as bright as the enhanced green fluorescent protein, is exceptionally photostable, used for biosensor development, and visible in living mice. Novel applications of smURFP include in vitro protein diagnostics with attomolar (10−18 M) sensitivity, encapsulation in viral particles, and fluorescent protein nanoparticles. However, the availability of biliverdin limits the fluorescence of biliverdin-attaching fluorescent proteins; hence, extra biliverdin is needed to enhance brightness. New methods for improved biliverdin bioavailability are necessary to develop improved bright far-red and near-infrared fluorescent proteins for noninvasive imaging in vivo.

Conceptualising the Benefit Framework of an Enterprise Content Management System (ECMS)

2018 ◽  
Vol 15 (2) ◽  
pp. 17
Author(s):  
Mohamad Rahimi Mohamad Rosman ◽  
Mohammad Azhan Abdul Aziz
Keyword(s):  
Management System ◽  
Content Management ◽  
Extensive Review ◽  
Content Management System ◽  
Field Of Study ◽  
Factors Influencing ◽  
Digital Format ◽  
Enterprise Content Management ◽  
The Subject

Content management is an organisational effort of managing content, particularly in digital format. Although it has been over 25 years since content management was introduced, this field of study is still considered an emerging topic with unresolved issues-in particular, the subject of benefit achievement. Therefore, grounded on an extensive review of 135 articles, the purpose of this study is to investigate the benefits that organisations can gain through the proper use of an Enterprise Content Management System (ECMS). Subsequently, this paper identifies a list of ECMS benefits and proposes an ECMS benefit framework for further exploration into this field. Our result shows that although ECMS does bring benefits to organisations, these benefits are diverse; indicating that there are certain determinants or factors influencing the achievement of such benefits. Moreover, it is also found that in the context of the benefit framework of Shang and Seddon [10], three categories were found relevant to the field of content management: operational benefit, managerial benefit, and strategic benefit.

THE BALANCE OF PROBABILITY: STATISTICS AND THE DIACHRONIC STUDY OF ANCIENT HEBREW

2017 ◽  
Vol 25 (2) ◽  
pp. 927-960
Author(s):  
Jarod Jacobs
Keyword(s):  
Dead Sea Scrolls ◽  
Dead Sea ◽  
Biblical Hebrew ◽  
Large Datasets ◽  
Dual Function ◽  
Statistical Tools ◽  
Masoretic Text ◽  
Linguistic Research ◽  
Recent Debate ◽  
Diachronic Study

In this article, I discuss three statistical tools that have proven pivotal in linguistic research, particularly those studies that seek to evaluate large datasets. These tools are the Gaussian Curve, significance tests, and hierarchical clustering. I present a brief description of these tools and their general uses. Then, I apply them to an analysis of the variations between the “biblical” DSS and our other witnesses, focusing upon variations involving particles. Finally, I engage the recent debate surrounding the diachronic study of Biblical Hebrew. This article serves a dual function. First, it presents statistical tools that are useful for many linguistic studies. Second, it develops an analysis of the he-locale, as it is used in the “biblical” Dead Sea Scrolls, Masoretic Text, and Samaritan Pentateuch. Through that analysis, this article highlights the value of inferential statistical tools as we attempt to better understand the Hebrew of our ancient witnesses.

Colloidal Plasmonic Nanostar Antennas with Wide Range Resonance Tunability

2019 ◽  
Author(s):  
Theodoros Tsoulos ◽  
Supriya Atta ◽  
Maureen Lagos ◽  
Michael Beetz ◽  
Philip Batson ◽  
...  
Keyword(s):  
Single Particle ◽  
Structural Complexity ◽  
Field Enhancement ◽  
Hot Electron ◽  
Structure Property ◽  
Plasmon Band ◽  
Gold Nanostars ◽  
Wide Range ◽  
Particle Level ◽  
Spectrally Resolved

<div>Gold nanostars display exceptional field enhancement properties and tunable resonant modes that can be leveraged to create effective imaging tags or phototherapeutic agents, or to design novel hot-electron based photocatalysts. From a fundamental standpoint, they represent important tunable platforms to study the dependence of hot carrier energy and dynamics on plasmon band intensity and position. Toward the realization of these platforms, holistic approaches taking into account both theory and experiments to study the fundamental behavior of these</div><div>particles are needed. Arguably, the intrinsic difficulties underlying this goal stem from the inability to rationally design and effectively synthesize nanoparticles that are sufficiently monodispersed to be employed for corroborations of the theoretical results without the need of single particle experiments. Herein, we report on our concerted computational and experimental effort to design, synthesize, and explain the origin and morphology-dependence of the plasmon modes of a novel gold nanostar system, with an approach that builds upon the well-known plasmon hybridization model. We have synthesized monodispersed samples of gold nanostars with finely tunable morphology employing seed-mediated colloidal protocols, and experimentally observed narrow and spectrally resolved harmonics of the primary surface plasmon resonance mode both at the single particle level (via electron energy loss spectroscopy) and in ensemble (by UV-Vis and ATR-FTIR spectroscopies). Computational results on complex anisotropic gold nanostructures are validated experimentally on samples prepared colloidally, underscoring their importance as ideal testbeds for the study of structure-property relationships in colloidal nanostructures of high structural complexity.</div>

Pulse and Progress of Venture Capital Financing in India: An Analytical Study

Think India ◽  
2019 ◽  
Vol 22 (3) ◽  
pp. 553-562
Author(s):  
Dr. Devarajappa S
Keyword(s):  
Venture Capital ◽  
Capital Investment ◽  
Analytical Study ◽  
Economic Empowerment ◽  
Statistical Tools ◽  
Venture Capital Investment ◽  
Secondary Sources ◽  
Current Trends ◽  
Capital Financing ◽  
Secondary Information

The Main objective of the paper is to examine the current trends and progress of the venture capital in India and the paper also highlights the concept and stages of financing of venture capital. To meet the aim objective of the study the researcher used secondary sources. The required secondary information has been collected through various articles, reports, magazines’ and websites. To examine the trends of venture capital in India, IVCA (Indian Venture Capital Association) report is used.  For the purpose of examine the data; the statistical tools like Mean, Standard Deviation, Charts and ANOVA, Correlation coefficient have been employed.   The study concludes that, the venture capital investment has been increasing in India and this is the positive indication for the country, to curb the unemployment, economic empowerment of people through maximizing startups in India

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